The female Player Character is known as White. It has also been used in screenshots of her as another player; Black visits her World.
Don George and Swanna have both been called "Carl" for their slight resemblance to the Aqua Teen Hunger Force character while the new early bug, Sewaddle, is going by Countapillar, Bugleaf, Smugbug, Fraterpie, Collarpillar and Vampillar. A comparison.◊
Sarcophaghost for Cofagrigus. However, that exceeds the games' character limit, so coming up with shorter names is a bit of a pastime. Another is Koffin.
Thanks to people mishearing his battle theme, Ghetsis is often jokingly called "DENNIS". For a short while, it also applied to Genesect when dataminers assumed Ghetsis' battle music belonged to it. Other nicknames for Ghetsis include Geechisu, Geetis and (thanks to 4chan) Gaycheese.
"Pokémon Gray/Grey" for the third game that never happended.
"Plankster" "Jokirder" and "Clowncrete" for Timburr, Gurdurr, and Conkeldurr respectively. Timburr is also called Jonny quite a bit for that plank it carries around all the time.
The member of the Elite Four who uses Fighting types is Westley Snipes.
The Elite Four was nicknamed "Mystery Inc." due to a few resemblances to the titular Scooby Doo characters. Shauntal being Velma, Grimsley being Shaggy, Caitlin being Daphne, and Marshal being Fred.
Swoobat is the Derp Bat.
Stunfisk is Derpfish.
Ghetsis's Hydreigon has been dubbed Haxdreigon and variations thereof.
Similarly, quite a few fans have taken to calling Elesa's Emolgas "demons". Although this isn't so much a nickname as it is an insult.
Also from 4chan, Galvantula has been dubbed "Tarantesla".
Throh and Sawk get called Bert and Ernie a lot. Alternatively, Judo Jim and Karate Carl.
Thundurus is often referred to as "Thundy", while Landorus is often called Lando or Garfield.
Early on, rumors of a supposed "Swimming Goggles" item that raised the user's Special Attack and accuracy whle also putting non-Water-types to sleep circulated. However, no such item exists, Dummied Out or otherwise.
Dataminers initially believed that Bianca was the Champion, when this isn't the case (presumably, her post-League team was misinterpreted as a Champion team).
With Victini, Reshiram and Zekrom being the first Pokémon to be hard-coded into never being Shiny, many rumors on how to get them to appear as such — fueled by the existence of Shiny sprites for all three in the data — circulated. However, outside of hacking, it's impossible to get them (in the Gen V games, anyway).
Originally, Frillish and Jellicent were supposed to be just a pure Water-type species, but were changed to be Water/Ghost (a type combination that hasn't been seen prior to Generation V) for the sake of distribution. This resulted in their creator (a new artist working at Game Freak) being disappointed with the scary aspects (such as causing ships that cross its habitat to be sunken and all of the passengers on board to end up missing) being added to what was supposed to just be some normal jellyfish based on princes and princesses.
Stunfisk was also supposed to be a Electric/Water-type. This was changed for the sake of type distribution.
Deino, Zweilous and Hydreigon were originally intended to be cybernetic dragons incorporating aspects of tanks within their bodies. The track-like markings on their bellies seem to be a remnant of this.